Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

Barbato, Marta; Mapelli, Francesca; Magagnini, Mirko; Chouaia, Bessem; Armeni, Monica; Marasco, Ramona; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

doi:10.1016/j.marpolbul.2016.01.029

Cited by 29 publications

(13 citation statements)

References 46 publications

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“…As the original enrichment was generated from a dilbit spill, our data suggest that dilbit degradation may be faster in freshwater environments that have previously been exposed to crude oil hydrocarbons, as the environment may be selecting for bacterial communities capable of a rapid response [70]. These findings are also relevant to those interested in exploring the potential of autochthonous microbial consortia in bioaugmentation studies [71]. Sequencing analyses identified several bacteria that have previously been identified as hydrocarbon degraders, some of which have been detected in both freshwater and marine systems (e.g., Hydrogenophaga, Alcalinovorax, Novosphingobium, Pseudomonas, Dokdonella, Parvibaculum, Microbacterium).…”

Section: Discussionmentioning

confidence: 74%

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments

Deshpande

Sundaravadivelu

Techtmann

et al. 2018

Journal of Hazardous Materials

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Treatability experiments were conducted to determine the biodegradation of diluted bitumen (dilbit) at 5 and 25 °C for 72 and 60 days, respectively. Microbial consortia obtained from the Kalamazoo River Enbridge Energy spill site were enriched on dilbit at both 5 (cryo) and 25 (meso) ºC. On every sampling day, triplicates were sacrificed and residual hydrocarbon concentrations (alkanes and polycyclic aromatic hydrocarbons) were determined by GCMS/MS. The composition and relative abundance of different bacterial groups were identified by 16S rRNA gene sequencing analysis. While some physicochemical differences were observed between the two dilbits, their biodegradation profiles were similar. The rates and extent of degradation were greater at 25 °C. Both consortia metabolized 99.9% of alkanes; however, the meso consortium was more effective at removing aromatics than the cryo consortium (97.5 vs 70%). Known hydrocarbon-degrading bacteria were present in both consortia (Pseudomonas, Rhodococcus, Hydrogenophaga, Parvibaculum, Arthrobacter, Acidovorax), although their relative abundances depended on the temperatures at which they were enriched. Regardless of the dilbit type, the microbial community structure significantly changed as a response to the diminishing hydrocarbon load. Our results demonstrate that dilbit can be effectively degraded by autochthonous microbial consortia from sites with recent exposure to dilbit contamination.

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Section: Discussionmentioning

confidence: 74%

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments

Deshpande

Sundaravadivelu

Techtmann

et al. 2018

Journal of Hazardous Materials

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“…This phylum is divided into five major classes, all with oil-degrading genera ( Gao et al, 2014 ). On the whole, isolated bacteria where ascribed mainly to genera belonging to Gamma-proteobacteria class, whose dominance within the enriched microcosms can be expected since it comprises many of the hydrocarbonoclastic bacteria responsible for the first steps of hydrocarbons degradation ( Head et al, 2006 ; Yakimov et al, 2007 ; Barbato et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi

et al. 2018

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Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0–1, 1–2, 2–3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.

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“…In these works, the involvement of and Karlson, 2005;Simarro et al, 2013) Similar to the report by Simarro et al (2013) the heterotrophic bacteria counts were two orders of magnitude higher than contaminant-degrading bacteria. It has been reported that the soil microbial population changes with the addition of a contaminant (Yan et al, 2016) and that a specific microorganism selection takes place (Barbato et al, 2016). Furthermore, the ring structure are supported by Yang et al (2010), who indicated that sequestration is the major mechanism for the accumulation of PAHs in soils.…”

Section: Discussionmentioning

confidence: 96%

Adsorption and native microbiota of an agricultural soil are involved in the removal of fluoranthene

Hernández‐Hernández

Evaristo-Vázquez

Vásquez-Murrieta

et al. 2016

J. Soil Sci. Plant Nutr.

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Several factors can influence the removal of polycyclic aromatic hydrocarbons from agricultural soils, such as the native microbiota, the physicochemical properties of the soil, soil management and addition of exogenous microorganisms. Nevertheless, the involvement of these factors has not been studied during fluoranthene removal at the microcosm level. In the present study, the effects of these factors were evaluated in microcosms composed of an organic agricultural soil (OAS-microcosm) and conventional agricultural soil (CAS-microcosm) contaminated with fluoranthene. According to their physicochemical properties, both soils were classified as silt loam. They had similar cation exchange capacities, water holding capacities and P-PO4 3-, but different pHs, electrical conductivities, and percentages of N, C, silt, clay and sand. Fluoranthene did not alter the native microbiota of the OAS-and CAS-microcosm because similar banding profiles were obtained in PCR-DGGE analysis of the 16S rRNA gene, and the total heterotrophic bacteria count as well as fluoranthene-degrading bacteria count were similar between microcosms with fluoranthene and their controls without fluoranthene. However, OAS-and CAS-microcosms showed higher respiratory activity than their controls (p<0.05). At the beginning of the degradation kinetics, OAS-and CAS-microcosms reached a higher percentage of fluoranthene removal than their abiotic counterparts (adsorption controls; p<0.05); towards the end of the degradation kinetics, no significant difference was observed between the OAS-and CAS-microcosms and their corresponding adsorption controls. The bioaugmentation assay using a fluoranthene-degrading bacterial consortium increased fluoranthene removal. This work showed that fluoranthene adsorption to soil and native microbiota of agricultural soils were involved in fluoranthene removal.

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Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

Cited by 29 publications

References 46 publications

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments

Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi

Adsorption and native microbiota of an agricultural soil are involved in the removal of fluoranthene

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